Examples with AnnotationSet gate.AnnotationSet used on opensource projects

Example 1 with AnnotationSet

use of gate.AnnotationSet in project gate-core by GateNLP.

the class LuceneDocument method createDocuments.

/**
 * Given an instance of Gate Document, it converts it into the format that
 * lucene can understand and can store in its indexes. This method also stores
 * the tokenStream on the disk in order to retrieve it at the time of
 * searching
 */
public List<Document> createDocuments(String corpusPersistenceID, gate.Document gateDoc, String documentID, List<String> annotSetsToInclude, List<String> annotSetsToExclude, List<String> featuresToInclude, List<String> featuresToExclude, String indexLocation, String baseTokenAnnotationType, Boolean createTokensAutomatically, String indexUnitAnnotationType) {
    if (baseTokenAnnotationType != null)
        baseTokenAnnotationType = baseTokenAnnotationType.trim();
    List<Document> toReturnBack = new ArrayList<Document>();
    List<String> annotSetsToIndex = new ArrayList<String>();
    // about annotation sets to exclude
    if (annotSetsToInclude.size() > 0) {
        annotSetsToIndex = annotSetsToInclude;
    // if there's only one annotation to index, we don't need to
    // create a MergeSet
    // if(annotSetsToIndex.size() == 1) createMergeSet = false;
    } else if (annotSetsToExclude.size() > 0) {
        // if there were no annotation sets to include, check if user has
        // provided any annotation sets to exclude
        // if so, we need to index all annotation sets but provided in the
        // annotationsetstoexclude list
        Set<String> namedAnnotSets = new HashSet<String>();
        if (gateDoc.getNamedAnnotationSets() != null && gateDoc.getNamedAnnotationSets().keySet() != null) {
            namedAnnotSets = gateDoc.getNamedAnnotationSets().keySet();
        }
        for (String setName : namedAnnotSets) {
            if (annotSetsToExclude.contains(setName))
                continue;
            annotSetsToIndex.add(setName);
        }
        if (!annotSetsToExclude.contains(Constants.DEFAULT_ANNOTATION_SET_NAME)) {
            annotSetsToIndex.add(Constants.DEFAULT_ANNOTATION_SET_NAME);
        }
    } else {
        // if both annotation sets to include and annotation sets to
        // exclude are empty
        // we need to index all annotation sets
        Set<String> namedAnnotSets = new HashSet<String>();
        if (gateDoc.getNamedAnnotationSets() != null && gateDoc.getNamedAnnotationSets().keySet() != null) {
            namedAnnotSets = gateDoc.getNamedAnnotationSets().keySet();
        }
        for (String setName : namedAnnotSets) {
            annotSetsToIndex.add(setName);
        }
        annotSetsToIndex.add(Constants.DEFAULT_ANNOTATION_SET_NAME);
    }
    // lets find out the annotation set that contains tokens in it
    AnnotationSet baseTokenAnnotationSet = null;
    // search in annotation sets to find out which of them has the
    // baseTokenAnnotationType annotations
    // initially this is set to false
    boolean searchBaseTokensInAllAnnotationSets = false;
    boolean searchIndexUnitInAllAnnotationSets = false;
    // this variable tells whether we want to create manual tokens or
    // not
    boolean createManualTokens = false;
    // lets check if user's input is setName.basetokenAnnotationType
    int index = -1;
    if (baseTokenAnnotationType != null && baseTokenAnnotationType.length() > 0)
        index = baseTokenAnnotationType.lastIndexOf('.');
    // basetokenAnnotationType
    if (index >= 0) {
        // set name
        String setName = baseTokenAnnotationType.substring(0, index);
        // token type
        baseTokenAnnotationType = baseTokenAnnotationType.substring(index + 1, baseTokenAnnotationType.length());
        // annotation set
        if (setName.equals(Constants.DEFAULT_ANNOTATION_SET_NAME))
            baseTokenAnnotationSet = gateDoc.getAnnotations().get(baseTokenAnnotationType);
        else
            baseTokenAnnotationSet = gateDoc.getAnnotations(setName).get(baseTokenAnnotationType);
        // base token annotation type
        if (baseTokenAnnotationSet == null || baseTokenAnnotationSet.size() == 0) {
            System.err.println("Base Tokens " + baseTokenAnnotationType + " counldn't be found under the specified annotation set " + setName + "\n searching them in other annotation sets");
            searchBaseTokensInAllAnnotationSets = true;
        }
    } else {
        // either baseTokenAnnotation type is null or user hasn't provided
        // any annotaiton set name
        // so we search in all annotation sets
        searchBaseTokensInAllAnnotationSets = true;
    }
    if (baseTokenAnnotationType != null && baseTokenAnnotationType.length() > 0 && searchBaseTokensInAllAnnotationSets) {
        // we set this to true and if we find basetokens in any of the
        // annotationsets to index
        // we will set this to false
        createManualTokens = true;
        for (String aSet : annotSetsToIndex) {
            if (aSet.equals(Constants.DEFAULT_ANNOTATION_SET_NAME)) {
                AnnotationSet tempSet = gateDoc.getAnnotations().get(baseTokenAnnotationType);
                if (tempSet.size() > 0) {
                    baseTokenAnnotationSet = tempSet;
                    // System.out.println("found in default annotation set");
                    createManualTokens = false;
                    break;
                }
            } else {
                AnnotationSet tempSet = gateDoc.getAnnotations(aSet).get(baseTokenAnnotationType);
                if (tempSet.size() > 0) {
                    baseTokenAnnotationSet = tempSet;
                    // System.out.println("found in "+aSet);
                    createManualTokens = false;
                    break;
                }
            }
        }
    }
    // we'll have to create tokens ourselves
    if (baseTokenAnnotationType == null || baseTokenAnnotationType.length() == 0)
        createManualTokens = true;
    // lets check if we have to create ManualTokens
    if (createManualTokens) {
        if (!createTokensAutomatically.booleanValue()) {
            System.out.println("Tokens couldn't be found in the document - Ignoring the document " + gateDoc.getName());
            return null;
        }
        baseTokenAnnotationType = Constants.ANNIC_TOKEN;
        if (baseTokenAnnotationSet == null) {
            baseTokenAnnotationSet = new AnnotationSetImpl(gateDoc);
        }
        if (!createTokens(gateDoc, baseTokenAnnotationSet)) {
            System.out.println("Tokens couldn't be created manually - Ignoring the document " + gateDoc.getName());
            return null;
        }
    }
    // by now, baseTokenAnnotationSet will not be null for sure and we
    // know what's the baseTokenAnnotationType
    // lets find out the annotation set that contains
    // indexUnitAnnotationType in it
    AnnotationSet indexUnitAnnotationSet = null;
    // lets check if user has provided setName.indexUnitAnnotationType
    index = -1;
    if (indexUnitAnnotationType != null && indexUnitAnnotationType.trim().length() > 0)
        index = indexUnitAnnotationType.lastIndexOf('.');
    // indexUnitAnnotationType
    if (index >= 0) {
        // setName
        String setName = indexUnitAnnotationType.substring(0, index);
        // indexUnitAnnotationType
        indexUnitAnnotationType = indexUnitAnnotationType.substring(index + 1, indexUnitAnnotationType.length());
        if (setName.equals(Constants.DEFAULT_ANNOTATION_SET_NAME))
            indexUnitAnnotationSet = gateDoc.getAnnotations().get(indexUnitAnnotationType);
        else
            indexUnitAnnotationSet = gateDoc.getAnnotations(setName).get(indexUnitAnnotationType);
        // if so, we'll have to search other annotation sets
        if (indexUnitAnnotationSet == null || indexUnitAnnotationSet.size() == 0) {
            System.err.println("Index Unit " + indexUnitAnnotationType + " counldn't be found under the specified annotation set " + setName + "\n searching them in other annotation sets");
            searchIndexUnitInAllAnnotationSets = true;
        }
    } else {
        // either indexUnitAnnotationType is null or user hasn't provided
        // the setname
        searchIndexUnitInAllAnnotationSets = true;
    }
    // searching in all annotation set names
    if (indexUnitAnnotationType != null && indexUnitAnnotationType.length() > 0 && searchIndexUnitInAllAnnotationSets) {
        for (String aSet : annotSetsToIndex) {
            if (aSet.equals(Constants.DEFAULT_ANNOTATION_SET_NAME)) {
                AnnotationSet tempSet = gateDoc.getAnnotations().get(indexUnitAnnotationType);
                if (tempSet.size() > 0) {
                    indexUnitAnnotationSet = tempSet;
                    break;
                }
            } else {
                AnnotationSet tempSet = gateDoc.getAnnotations(aSet).get(indexUnitAnnotationType);
                if (tempSet.size() > 0) {
                    indexUnitAnnotationSet = tempSet;
                    break;
                }
            }
        }
    }
    // to null as well
    if (indexUnitAnnotationSet == null) {
        indexUnitAnnotationType = null;
    }
    int j = 0;
    for (String annotSet : annotSetsToIndex) {
        // we need to generate the Token Stream here, and send it to the
        // GateLuceneReader
        AnnotationSet aSetToIndex = annotSet.equals(Constants.DEFAULT_ANNOTATION_SET_NAME) ? gateDoc.getAnnotations() : gateDoc.getAnnotations(annotSet);
        Set<String> indexedFeatures = new HashSet<String>();
        // tempBaseTokenAnnotationSet is not null
        List<Token>[] tokenStreams = getTokens(gateDoc, aSetToIndex, featuresToInclude, featuresToExclude, baseTokenAnnotationType, baseTokenAnnotationSet, indexUnitAnnotationType, indexUnitAnnotationSet, indexedFeatures);
        // tokenStream is set to null
        if (tokenStreams == null)
            return null;
        // this is enabled only if there are more than one annotation sets
        // available to search in
        // if(createMergeSet) {
        // if(mergedSet == null) mergedSet = new AnnotationSetImpl(gateDoc);
        // 
        // // we need to merge all annotations but the
        // // baseTokenAnnotationType
        // for(String aType : aSetToIndex.getAllTypes()) {
        // 
        // if(aType.equals(baseTokenAnnotationType)) {
        // continue;
        // }
        // 
        // if(indexUnitAnnotationType != null
        // && aType.equals(indexUnitAnnotationType)) {
        // continue;
        // }
        // 
        // for(Annotation a : aSetToIndex.get(aType)) {
        // try {
        // mergedSet.add(a.getStartNode().getOffset(), a.getEndNode()
        // .getOffset(), a.getType(), a.getFeatures());
        // }
        // catch(InvalidOffsetException ioe) {
        // throw new GateRuntimeException(ioe);
        // }
        // }
        // 
        // }
        // }
        StringBuffer indexedFeaturesString = new StringBuffer();
        for (String aFeat : indexedFeatures) {
            indexedFeaturesString.append(aFeat + ";");
        }
        Document[] toReturn = new Document[tokenStreams.length];
        for (int i = 0; i < tokenStreams.length; i++, j++) {
            // make a new, empty document
            Document doc = new Document();
            // and then create the document
            LuceneReader reader = new LuceneReader(gateDoc, tokenStreams[i]);
            doc.add(Field.Keyword(Constants.DOCUMENT_ID, documentID));
            doc.add(Field.Keyword(Constants.DOCUMENT_ID_FOR_SERIALIZED_FILE, documentID + "-" + j));
            doc.add(Field.Keyword(Constants.INDEXED_FEATURES, indexedFeaturesString.substring(0, indexedFeaturesString.length() - 1)));
            if (corpusPersistenceID != null)
                doc.add(Field.Keyword(Constants.CORPUS_ID, corpusPersistenceID));
            doc.add(Field.Keyword(Constants.ANNOTATION_SET_ID, annotSet));
            doc.add(Field.Text("contents", reader));
            // here we store token stream on the file system
            try {
                writeOnDisk(tokenStreams[i], documentID, documentID + "-" + j, indexLocation);
            } catch (Exception e) {
                Err.println("\nIgnoring the document : " + gateDoc.getName() + " since its token stream cannot be written on the disk");
                Err.println("Reason: " + e.getMessage());
                return null;
            }
            // return the document
            toReturn[i] = doc;
        }
        toReturnBack.addAll(Arrays.asList(toReturn));
    }
    return toReturnBack;
}

Example 2 with AnnotationSet

use of gate.AnnotationSet in project gate-core by GateNLP.

the class CorefEditor method initGUI.

/**
 * This method intiates the GUI for co-reference editor
 */
@Override
protected void initGUI() {
    // get a pointer to the textual view used for highlights
    Iterator<DocumentView> centralViewsIter = owner.getCentralViews().iterator();
    while (textView == null && centralViewsIter.hasNext()) {
        DocumentView aView = centralViewsIter.next();
        if (aView instanceof TextualDocumentView)
            textView = (TextualDocumentView) aView;
    }
    textPane = (JTextArea) ((JScrollPane) textView.getGUI()).getViewport().getView();
    highlighter = textPane.getHighlighter();
    chainToolTipAction = new ChainToolTipAction();
    chainToolTipTimer = new javax.swing.Timer(500, chainToolTipAction);
    chainToolTipTimer.setRepeats(false);
    newCorefAction = new NewCorefAction();
    newCorefActionTimer = new javax.swing.Timer(500, newCorefAction);
    newCorefActionTimer.setRepeats(false);
    colorGenerator = new ColorGenerator();
    // main Panel
    mainPanel = new JPanel();
    mainPanel.setLayout(new BorderLayout());
    // topPanel
    topPanel = new JPanel();
    topPanel.setLayout(new BorderLayout());
    // subPanel
    subPanel = new JPanel();
    subPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
    // showAnnotations Button
    showAnnotations = new JToggleButton("Show");
    showAnnotations.addActionListener(this);
    // annotSets
    annotSets = new JComboBox<String>();
    annotSets.addActionListener(this);
    // get all the annotationSets
    Map<String, AnnotationSet> annotSetsMap = document.getNamedAnnotationSets();
    annotSetsModel = new DefaultComboBoxModel<String>();
    if (annotSetsMap != null) {
        String[] array = annotSetsMap.keySet().toArray(new String[annotSetsMap.keySet().size()]);
        for (int i = 0; i < array.length; i++) {
            annotSetsMap.get(array[i]).addAnnotationSetListener(this);
        }
        annotSetsModel = new DefaultComboBoxModel<String>(array);
    }
    document.getAnnotations().addAnnotationSetListener(this);
    annotSetsModel.insertElementAt(DEFAULT_ANNOTSET_NAME, 0);
    annotSets.setModel(annotSetsModel);
    // annotTypes
    annotTypesModel = new DefaultComboBoxModel<String>();
    annotTypes = new JComboBox<String>(annotTypesModel);
    annotTypes.addActionListener(this);
    subPanel.add(new JLabel("Sets : "));
    subPanel.add(annotSets);
    JPanel tempPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
    tempPanel.add(new JLabel("Types : "));
    tempPanel.add(annotTypes);
    tempPanel.add(showAnnotations);
    // intialises the Data
    initData();
    // and creating the tree
    corefTree = new JTree(rootNode);
    corefTree.putClientProperty("JTree.lineStyle", "None");
    corefTree.setRowHeight(corefTree.getRowHeight() * 2);
    corefTree.setLargeModel(true);
    corefTree.setAutoscrolls(true);
    // corefTree.setRootVisible(false);
    // corefTree.setShowsRootHandles(false);
    corefTree.addMouseListener(new CorefTreeMouseListener());
    corefTree.setCellRenderer(new CorefTreeCellRenderer());
    mainPanel.add(topPanel, BorderLayout.NORTH);
    mainPanel.add(new JScrollPane(corefTree), BorderLayout.CENTER);
    topPanel.add(subPanel, BorderLayout.CENTER);
    topPanel.add(tempPanel, BorderLayout.SOUTH);
    // get the highlighter
    textPaneMouseListener = new TextPaneMouseListener();
    annotSets.setSelectedIndex(0);
    // finally show the tree
    // annotSetSelectionChanged();
    document.addDocumentListener(this);
    document.getFeatures().addFeatureMapListener(this);
}

Example 3 with AnnotationSet

use of gate.AnnotationSet in project gate-core by GateNLP.

the class CorpusQualityAssurance method readSetsTypesFeatures.

/**
 * Update set lists.
 * @param documentStart first document to read in the corpus,
 * the first document of the corpus is 0.
 */
protected void readSetsTypesFeatures(final int documentStart) {
    if (!isShowing()) {
        return;
    }
    corpusChanged = false;
    SwingUtilities.invokeLater(new Runnable() {

        @Override
        public void run() {
            progressBar.setMaximum(corpus.size() - 1);
            progressBar.setString("Read sets, types, features");
            reloadCacheAction.setEnabled(false);
        }
    });
    CorpusQualityAssurance.this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    Runnable runnable = new Runnable() {

        @Override
        public void run() {
            if (docsSetsTypesFeatures.size() != corpus.getDocumentNames().size() || !docsSetsTypesFeatures.keySet().containsAll(corpus.getDocumentNames())) {
                if (documentStart == 0) {
                    docsSetsTypesFeatures.clear();
                }
                TreeMap<String, TreeMap<String, TreeSet<String>>> setsTypesFeatures;
                TreeMap<String, TreeSet<String>> typesFeatures;
                TreeSet<String> features;
                for (int i = documentStart; i < corpus.size(); i++) {
                    // fill in the lists of document, set, type and feature names
                    boolean documentWasLoaded = corpus.isDocumentLoaded(i);
                    Document document = corpus.get(i);
                    if (document != null && document.getAnnotationSetNames() != null) {
                        setsTypesFeatures = new TreeMap<String, TreeMap<String, TreeSet<String>>>(collator);
                        HashSet<String> setNames = new HashSet<String>(document.getAnnotationSetNames());
                        setNames.add("");
                        for (String set : setNames) {
                            typesFeatures = new TreeMap<String, TreeSet<String>>(collator);
                            AnnotationSet annotations = document.getAnnotations(set);
                            for (String type : annotations.getAllTypes()) {
                                features = new TreeSet<String>(collator);
                                for (Annotation annotation : annotations.get(type)) {
                                    for (Object featureKey : annotation.getFeatures().keySet()) {
                                        features.add((String) featureKey);
                                    }
                                }
                                typesFeatures.put(type, features);
                            }
                            setsTypesFeatures.put(set, typesFeatures);
                        }
                        docsSetsTypesFeatures.put(document.getName(), setsTypesFeatures);
                    }
                    if (!documentWasLoaded) {
                        corpus.unloadDocument(document);
                        Factory.deleteResource(document);
                    }
                    final int progressValue = i + 1;
                    SwingUtilities.invokeLater(new Runnable() {

                        @Override
                        public void run() {
                            progressBar.setValue(progressValue);
                            if ((progressValue + 1) % 5 == 0) {
                                // update the set list every 5 documents read
                                updateSetList();
                            }
                        }
                    });
                    if (Thread.interrupted()) {
                        return;
                    }
                }
            }
            updateSetList();
            SwingUtilities.invokeLater(new Runnable() {

                @Override
                public void run() {
                    progressBar.setValue(progressBar.getMinimum());
                    progressBar.setString("");
                    CorpusQualityAssurance.this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
                    reloadCacheAction.setEnabled(true);
                }
            });
        }
    };
    readSetsTypesFeaturesThread = new Thread(runnable, "readSetsTypesFeatures");
    readSetsTypesFeaturesThread.setPriority(Thread.MIN_PRIORITY);
    readSetsTypesFeaturesThread.start();
}

Example 4 with AnnotationSet

use of gate.AnnotationSet in project gate-core by GateNLP.

the class CorpusQualityAssurance method compareAnnotation.

protected void compareAnnotation() {
    int progressValuePrevious = -1;
    if (readSetsTypesFeaturesThread != null && readSetsTypesFeaturesThread.isAlive()) {
        // stop the thread that reads the sets, types and features
        progressValuePrevious = progressBar.getValue();
        readSetsTypesFeaturesThread.interrupt();
    }
    SwingUtilities.invokeLater(new Runnable() {

        @Override
        public void run() {
            progressBar.setMaximum(corpus.size() - 1);
            progressBar.setString("Compare annotations");
            setList.setEnabled(false);
            setCheck.setEnabled(false);
            typeList.setEnabled(false);
            typeCheck.setEnabled(false);
            featureList.setEnabled(false);
            featureCheck.setEnabled(false);
            optionsButton.setEnabled(false);
            measureTabbedPane.setEnabled(false);
            measureList.setEnabled(false);
            exportToHtmlAction.setEnabled(false);
            reloadCacheAction.setEnabled(false);
        }
    });
    boolean useBdm = false;
    if (measuresType == FSCORE_MEASURES) {
        differsByDocThenType.clear();
        documentNames.clear();
        for (Object measure : measureList.getSelectedValues()) {
            if (((String) measure).contains("BDM")) {
                useBdm = true;
                break;
            }
        }
    }
    List<ClassificationMeasures> classificationMeasuresList = new ArrayList<ClassificationMeasures>();
    List<OntologyMeasures> documentOntologyMeasuresList = new ArrayList<OntologyMeasures>();
    List<OntologyMeasures> annotationOntologyMeasuresList = new ArrayList<OntologyMeasures>();
    // for each document
    for (int row = 0; row < corpus.size(); row++) {
        boolean documentWasLoaded = corpus.isDocumentLoaded(row);
        Document document = corpus.get(row);
        documentNames.add(document.getName());
        Set<Annotation> keys = new HashSet<Annotation>();
        Set<Annotation> responses = new HashSet<Annotation>();
        // get annotations from selected annotation sets
        if (keySetName.equals("[Default set]")) {
            keys = document.getAnnotations();
        } else if (document.getAnnotationSetNames() != null && document.getAnnotationSetNames().contains(keySetName)) {
            keys = document.getAnnotations(keySetName);
        }
        if (responseSetName.equals("[Default set]")) {
            responses = document.getAnnotations();
        } else if (document.getAnnotationSetNames() != null && document.getAnnotationSetNames().contains(responseSetName)) {
            responses = document.getAnnotations(responseSetName);
        }
        if (!documentWasLoaded) {
            // in case of datastore
            corpus.unloadDocument(document);
            Factory.deleteResource(document);
        }
        // add data to the fscore document table
        if (measuresType == FSCORE_MEASURES) {
            types.clear();
            for (Object type : typeList.getSelectedValues()) {
                types.add((String) type);
            }
            if (typeList.isSelectionEmpty()) {
                for (int i = 0; i < typeList.getModel().getSize(); i++) {
                    types.add((String) typeList.getModel().getElementAt(i));
                }
            }
            Set<String> featureSet = new HashSet<String>();
            for (Object feature : featureList.getSelectedValues()) {
                featureSet.add((String) feature);
            }
            HashMap<String, AnnotationDiffer> differsByType = new HashMap<String, AnnotationDiffer>();
            AnnotationDiffer differ;
            Set<Annotation> keysIter = new HashSet<Annotation>();
            Set<Annotation> responsesIter = new HashSet<Annotation>();
            for (String type : types) {
                if (!keys.isEmpty() && !types.isEmpty()) {
                    keysIter = ((AnnotationSet) keys).get(type);
                }
                if (!responses.isEmpty() && !types.isEmpty()) {
                    responsesIter = ((AnnotationSet) responses).get(type);
                }
                differ = new AnnotationDiffer();
                differ.setSignificantFeaturesSet(featureSet);
                // compare
                differ.calculateDiff(keysIter, responsesIter);
                differsByType.put(type, differ);
            }
            differsByDocThenType.add(differsByType);
            differ = new AnnotationDiffer(differsByType.values());
            List<String> measuresRow;
            if (useBdm) {
                OntologyMeasures ontologyMeasures = new OntologyMeasures();
                ontologyMeasures.setBdmFile(bdmFileUrl);
                ontologyMeasures.calculateBdm(differsByType.values());
                documentOntologyMeasuresList.add(ontologyMeasures);
                measuresRow = ontologyMeasures.getMeasuresRow(measureList.getSelectedValues(), documentNames.get(documentNames.size() - 1));
            } else {
                measuresRow = differ.getMeasuresRow(measureList.getSelectedValues(), documentNames.get(documentNames.size() - 1));
            }
            documentTableModel.addRow(measuresRow.toArray());
        // add data to the classification document table
        } else if (measuresType == CLASSIFICATION_MEASURES && !keys.isEmpty() && !responses.isEmpty()) {
            ClassificationMeasures classificationMeasures = new ClassificationMeasures();
            classificationMeasures.calculateConfusionMatrix((AnnotationSet) keys, (AnnotationSet) responses, (String) typeList.getSelectedValue(), (String) featureList.getSelectedValue(), verboseOptionCheckBox.isSelected());
            classificationMeasuresList.add(classificationMeasures);
            List<String> measuresRow = classificationMeasures.getMeasuresRow(measure2List.getSelectedValues(), documentNames.get(documentNames.size() - 1));
            document2TableModel.addRow(measuresRow.toArray());
            List<List<String>> matrix = classificationMeasures.getConfusionMatrix(documentNames.get(documentNames.size() - 1));
            for (List<String> matrixRow : matrix) {
                while (confusionTableModel.getColumnCount() < matrix.size()) {
                    confusionTableModel.addColumn(" ");
                }
                confusionTableModel.addRow(matrixRow.toArray());
            }
        }
        final int progressValue = row + 1;
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                progressBar.setValue(progressValue);
            }
        });
    }
    // add data to the fscore annotation table
    if (measuresType == FSCORE_MEASURES) {
        for (String type : types) {
            ArrayList<AnnotationDiffer> differs = new ArrayList<AnnotationDiffer>();
            for (HashMap<String, AnnotationDiffer> differsByType : differsByDocThenType) {
                differs.add(differsByType.get(type));
            }
            List<String> measuresRow;
            if (useBdm) {
                OntologyMeasures ontologyMeasures = new OntologyMeasures();
                ontologyMeasures.setBdmFile(bdmFileUrl);
                ontologyMeasures.calculateBdm(differs);
                annotationOntologyMeasuresList.add(ontologyMeasures);
                measuresRow = ontologyMeasures.getMeasuresRow(measureList.getSelectedValues(), type);
            } else {
                AnnotationDiffer differ = new AnnotationDiffer(differs);
                measuresRow = differ.getMeasuresRow(measureList.getSelectedValues(), type);
            }
            annotationTableModel.addRow(measuresRow.toArray());
        }
    }
    // add summary rows to the fscore tables
    if (measuresType == FSCORE_MEASURES) {
        if (useBdm) {
            OntologyMeasures ontologyMeasures = new OntologyMeasures(documentOntologyMeasuresList);
            printSummary(ontologyMeasures, documentTableModel, 5, documentTableModel.getRowCount(), measureList.getSelectedValues());
            ontologyMeasures = new OntologyMeasures(annotationOntologyMeasuresList);
            printSummary(ontologyMeasures, annotationTableModel, 5, annotationTableModel.getRowCount(), measureList.getSelectedValues());
        } else {
            List<AnnotationDiffer> differs = new ArrayList<AnnotationDiffer>();
            for (Map<String, AnnotationDiffer> differsByType : differsByDocThenType) {
                differs.addAll(differsByType.values());
            }
            AnnotationDiffer differ = new AnnotationDiffer(differs);
            printSummary(differ, documentTableModel, 5, documentTableModel.getRowCount(), measureList.getSelectedValues());
            printSummary(differ, annotationTableModel, 5, annotationTableModel.getRowCount(), measureList.getSelectedValues());
        }
    // add summary rows to the classification tables
    } else if (measuresType == CLASSIFICATION_MEASURES) {
        ClassificationMeasures classificationMeasures = new ClassificationMeasures(classificationMeasuresList);
        printSummary(classificationMeasures, document2TableModel, 3, document2TableModel.getRowCount(), measure2List.getSelectedValues());
        List<List<String>> matrix = classificationMeasures.getConfusionMatrix("Whole corpus");
        int insertionRow = 0;
        for (List<String> row : matrix) {
            while (confusionTableModel.getColumnCount() < matrix.size()) {
                confusionTableModel.addColumn(" ");
            }
            confusionTableModel.insertRow(insertionRow++, row.toArray());
        }
    }
    SwingUtilities.invokeLater(new Runnable() {

        @Override
        public void run() {
            progressBar.setValue(progressBar.getMinimum());
            progressBar.setString("");
            setList.setEnabled(true);
            setCheck.setEnabled(true);
            typeList.setEnabled(true);
            typeCheck.setEnabled(true);
            featureList.setEnabled(true);
            featureCheck.setEnabled(true);
            optionsButton.setEnabled(true);
            measureTabbedPane.setEnabled(true);
            measureList.setEnabled(true);
            exportToHtmlAction.setEnabled(true);
            reloadCacheAction.setEnabled(true);
        }
    });
    if (progressValuePrevious > -1) {
        // restart the thread where it was interrupted
        readSetsTypesFeatures(progressValuePrevious);
    }
}

Example 5 with AnnotationSet

use of gate.AnnotationSet in project gate-core by GateNLP.

the class RelationSetView method setTarget.

@Override
public void setTarget(Object target) {
    if (doc != null) {
        doc.removeDocumentListener(this);
        doc.getAnnotations().removeAnnotationSetListener(this);
        doc.getAnnotations().getRelations().removeRelationSetListener(this);
        for (String name : doc.getAnnotationSetNames()) {
            AnnotationSet as = doc.getAnnotations(name);
            as.removeAnnotationSetListener(this);
            as.getRelations().removeRelationSetListener(this);
        }
    }
    doc = (Document) target;
    doc.addDocumentListener(this);
    doc.getAnnotations().addAnnotationSetListener(this);
    doc.getAnnotations().getRelations().addRelationSetListener(this);
    for (String name : doc.getAnnotationSetNames()) {
        AnnotationSet as = doc.getAnnotations(name);
        as.addAnnotationSetListener(this);
        as.getRelations().addRelationSetListener(this);
    }
    refresh();
}